• Trans-Omics Facility

The Facility is a division of the NIBB Core Research Facilities organized jointly by NIBB and NIPS for the promotion of DNA and protein studies. The facility maintains a wide array of core research equipment, ranging from standard machinery (e.g. ultracentrifuges) to cutting edge tools (e.g. next generation DNA sequencers), which amount to 90 instruments in total. The facility is dedicated to fostering collaborations with researchers both at NIBB and other academic institutions worldwide through the provision of these tools as well as expertise. Our current focus is functional genomics. We also act as a bridge between experimental biology and bioinformatics by providing close consultation and training.
 
In 2021, we still suffered from the effects of the COVID-19 pandemic that hampered research activities worldwide. While we operated our facility placing the highest priority on users’ safety, we provided remote support for the facilities’ users and online communication with collaborators to sustain research projects. Such efforts resulted in 11 co-authored papers being published.

Representative Instruments

Genomics

The advent of next-generation sequencing (NGS) technologies is transforming modern biology thanks to ultra-high-throughput DNA sequencing. Utilizing HiSeq, NextSeq and MiSeq (Illumina), Sequel (PacificBio Sciences), and MinION and GridION (Oxford Nanopore Technologies), the Facility is committed to joint research aimed at exploring new yet otherwise inaccessible fields in basic biology. We have upgraded the Sequel instrument in 2021, which enabled a significant increase of the HiFi long read production.
 
During 2021, we carried out 53 NGS projects in collaboration with researchers from academic institutions throughout the world. These projects cover a wide range of species (bacteria, animals, plants, and fungi) including both model and non-model organisms, and various other applications such as genomic re-sequencing, RNA-seq, single-cell trnascriptome and ChIP-seq.
 

Figure 1. Next-generation sequencer
 

Proteomics

As is listed below, two types of mass spectrometers and two protein sequencers are used for proteome studies in our facility. In 2021, we analyzed approximately 600 samples with mass spectrometers and protein sequencers.

Figure 2. LC-MS/MS system
 

Other analytical instruments (excerpts)

• Annual Report 2021 （PDF）

Shigenobu, S., Hayashi, Y., Watanabe, D., Tokuda, G., Hojo, M. Y., Toga, K., Saiki, R., Yaguchi, H., Masuoka, Y., Suzuki, R., Suzuki, S., Kimura, M., Matsunami, M., Sugime, Y., Oguchi, K., Niimi, T., Gotoh, H., Hojo, M. K., Miyazaki, S., … Maekawa, K. (2022). Genomic and transcriptomic analyses of the subterranean termite Reticulitermes speratus: Gene duplication facilitates social evolution. Proc. Natl. Acad. Sci. USA 119, e2110361119. https://doi.org/10.1073/pnas.2110361119

Matsunami, M., Suzuki, M., Haramoto, Y., Fukui, A., Inoue, T., Yamaguchi, K., Uchiyama, I., Mori, K., Tashiro, K., Ito, Y., Takeuchi, T., Suzuki, K. T., Agata, K., Shigenobu, S., & Hayashi, T. (2019). A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology. DNA Res. 26, 217–229. https://doi.org/10.1093/dnares/dsz003

Fallon, T. R., Lower, S. E., Chang, C. H., Bessho-Uehara, M., Martin, G. J., Bewick, A. J., Behringer, M., Debat, H. J., Wong, I., Day, J. C., Suvorov, A., Silva, C. J., Stanger-Hall, K. F., Hall, D. W., Schmitz, R. J., Nelson, D. R., Lewis, S. M., Shigenobu, S., Bybee, S. M., … Weng, J. K. (2018). Firefly genomes illuminate parallel origins of bioluminescence in beetles. eLife, 7, e36495. https://doi.org/10.7554/elife.36495

Yamaoka, S., Nishihama, R., Yoshitake, Y., Ishida, S., Inoue, K., Saito, M., Okahashi, K., Bao, H., Nishida, H., Yamaguchi, K., Shigenobu, S., Ishizaki, K., Yamato, K. T., & Kohchi, T. (2018). Generative Cell Specification Requires Transcription Factors Evolutionarily Conserved in Land Plants. Curr. Biol. 28, 479-486.e5. https://doi.org/10.1016/j.cub.2017.12.053

Maeda, T., Kobayashi, Y., Kameoka, H., Okuma, N., Takeda, N., Yamaguchi, K., Bino, T., Shigenobu, S., & Kawaguchi, M. (2018). Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity in Rhizophagus irregularis. Commun. Biol. 1, 87. https://doi.org/10.1038/s42003-018-0094-7

Ando, T., Matsuda, T., Goto, K., Hara, K., Ito, A., Hirata, J., Yatomi, J., Kajitani, R., Okuno, M., Yamaguchi, K., Kobayashi, M., Takano, T., Minakuchi, Y., Seki, M., Suzuki, Y., Yano, K., Itoh, T., Shigenobu, S., Toyoda, A., & Niimi, T. (2018). Repeated inversions within a pannier intron drive diversification of intraspecific colour patterns of ladybird beetles. Nat. Commun. 9, 3843. https://doi.org/10.1038/s41467-018-06116-1

Professor SHIGENOBU, Shuji TEL: +81 564 55 7672  E-mail: shige@nibb.ac.jp